Computational Biologist @ Patch Bio. regulatory DNA, RNA | gene therapy | synthetic biology My ''professional'' twitter account. She/her.
New York
Joined October 2014
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Thrilled to share our research on designing better 3' UTRs for mRNA therapeutics and vaccines!
By integrating high-throughput stability assays, machine learning models, and mRNA domain expertise, we engineered 3' UTRs that improve mRNA stability and protein production in vivo.
Excited to share our recent work at @Ginkgo . TLDR: high quality mRNA stability data -> performant ML models -> design 3’UTRs that increase stability -> in vivo validated ML 3’UTRs beat benchmark. biorxiv.org/content/10.1101/…
Check out the manuscript for insights on the behavior of ML model architectures and design strategies when interpreting mRNA sequence,
And for important results on the translation of mRNA sequence activity between contexts -- a consistent challenge in therapeutic development.
Elise Flynn retweeted
Excited to share our recent work at @Ginkgo . TLDR: high quality mRNA stability data -> performant ML models -> design 3’UTRs that increase stability -> in vivo validated ML 3’UTRs beat benchmark. biorxiv.org/content/10.1101/…
Elise Flynn retweeted
🚨Our work on multi-modal, single-cell pooled CRISPR screens to study GWAS variant-to-function, STING-seq, is now out in @ScienceMagazine! Read on for 6⃣ of the main findings from our study, led by myself and co-advised by @nevillesanjana and @tuuliel! 🎉
science.org/doi/10.1126/scie…
Elise Flynn retweeted
Our newest chapter is out @nature! - Bestrophin-2 and glutamine synthetase form a complex for glutamate release
nature.com/articles/s41586-0…
last talk: Ruchi Iohia from @JesseAGillis lab talking about chromatin interactions. Does a meta-analysis of Hi-C experiments, and found it did a better job of capturing interactions as validated by eQTLs gene co-expression: especially trans effects! #ashg22
preprint here: biorxiv.org/content/10.1101/…
Now @riley_mangan using single cell in vivo brain MPRA to find regulatory effects of human accelerated region (HAR) regulatory elements. Finds hominin-specific and cell-type-specific effects! #ashg22
Maya Bose from @theparkerlab with a talk about position-dependent effects of regulatory elements in an MPRA. Many TFBSs had larger effect upstream of promoter vs. downstream (including E2F, ETS), and activity was heavily biased for the forward strand #ashg22
@bowennjin finished up a great talk of promoter kinetics in cell lines: TF binding influences transcriptional burst frequency, not burst size. If frequency/size have opposite effects, they may be masked in classic eQTL studies #ashg22
preprint here for a much better explanation: biorxiv.org/content/10.1101/… (tweeting is hard)
Elise Flynn retweeted
Great meeting of the @GeneticsSociety Program Committee! It was an intense 1.5 days but we have an exciting program coming up for you. See you all in Los Angeles in October. – at North Bethesda, MD
Alternatively, if reading's not your thing, you can listen to some of my friends and family explain eQTLs after listening to my defense.
Have you wondered what eQTLs are or how they work?? @tuuliel_lab and I wrote a review about determining causal variants, elucidating molecular mechanisms, and understanding the context variability of eQTLs. annualreviews.org/doi/abs/10…
Elise Flynn retweeted
Which transcription factors (TF) regulate which #genetic variants?
Flynn et al analyze eQTL effect size as a function of TF level, & find candidate TF mechanisms for a large number of eQTLs
@EliseScience @tuuliel_lab @Pejminister @nygenome
doi.org/10.1371/journal.pgen…